Plot of the posterior probability of healthcare-associated infection (HCAI) for (a) Glasgow and (b) Sheffield hospital onset COVID-19 infection cases from the sequence reporting tool algorithm …
In cases where there are no close sequence matches in the dataset (including among community cases), the results returned are based solely on the priors and the metadata; this explains the fact that …
The black lines represent the time from admission to sampling. The values below the line are the posterior probability for unit infection + the posterior probability of hospital infection from the …
The tree tip nodes are coloured according to ward locations. The black lines represent the time from admission to sampling. The values below the line are the posterior probability for unit infection …
Also displayed are the proportion of sequenced cases in the three focus hospitals subdivided by assessment and inpatient locations (B), and the proportion of hospital onset COVID-19 infection (HOCI) …
Locations are analysed using only the outer postcode, and as such random jitter (within longitude and latitude of 0.05) has been added to allow display without overlap of points. Plot created using …
The circles with numbers represent the number of community sequences that are identical and at the base of each lineage (n = 5, n = 35, n = 4). Tree tips with black circles represent further …
Glasgow data | Sheffield data | |||||
---|---|---|---|---|---|---|
IPC classification | IPC classification | |||||
Indeterminate HCAI | Probable HCAI | Definite HCAI | Indeterminate HCAI | Probable HCAI | Definite HCAI | |
n HOCI cases | 20 | 27 | 78 | 62 | 68 | 71 |
Time from admission to sample*, days | 4.5 (3–6) | 11 (9-13) | 48 (26-83) | 5 (4–6) | 9 (8–13) | 22 (17–31) |
Summary of sequence matches returned for each HOCI case | ||||||
Close sequence match on ward | 5 (25.0) | 15 (55.6) | 53 (68.0) | 24 (38.7) | 46 (67.6) | 46 (64.8) |
No close sequence match on ward, but match within hospital | 8 (40.0) | 7 (25.9) | 19 (24.4) | 34 (54.8) | 21 (30.9) | 21 (29.6) |
No close sequence match anywhere within hospital | 7 (35.0) | 5 (18.5) | 6 (7.7) | 4 (6.5) | 1 (1.5) | 4 (5.6) |
Close sequence match to one or more HCW | 1 (5.0) | 0 (0) | 13 (16.7) | 55 (88.7) | 61 (89.7) | 59 (83.1) |
No close sequence match anywhere within dataset | 2 (10.0) | 1 (3.7) | 4 (5.1) | 4 (6.5) | 1 (1.5) | 4 (5.6) |
Probability calculations | ||||||
Prior probability of HCAI† | 0.39 (0.11–0.66) | 0.97 (0.92–0.99) | 1.00 (1.00–1.00) | 0.49 (0.29–0.66) | 0.92 (0.86–0.99) | 1.00 (1.00–1.00) |
Posterior probability of HCAI‡ | 0.33 (0.02–0.67) | 0.98 (0.96–1.00) | 1.00 (1.00–1.00) | 0.40 (0.11–0.80) | 0.98 (0.93–1.00) | 1.00 (0.99–1.00) |
Posterior probability of HCAI‡ category | ||||||
Low (<30%) | 10 (50.0) | 4 (14.8) | 2 (2.6) | 25 (40.3) | 0 (0) | 0 (0) |
Moderately low (≥30% and <50%) | 2 (10.0) | 0 (0) | 0 (0) | 12 (19.4) | 0 (0) | 0 (0) |
Medium (≥50% and <70%) | 4 (20.0) | 0 (0) | 0 (0) | 4 (6.5) | 5 (7.4) | 3 (4.2) |
High (≥70% and <85%) | 3 (15.0) | 0 (0) | 0 (0) | 8 (12.9) | 7 (10.3) | 2 (2.8) |
Very high (≥85%) | 1 (5.0) | 23 (85.2) | 76 (97.4) | 13 (21.0) | 56 (82.4) | 66 (93.0) |
Data shown as median (interquartile range) or n (%).
*Or first +ve test where known.
†Based on time from admission.
‡From source on ward or within hospital.
HCAI: healthcare-associated infection; HOCI: hospital onset COVID-19 infection; HCW: healthcare worker; IPC: infection prevention and control.
Glasgow data | Sheffield data | |
---|---|---|
n HOCI cases | 125 | 201 |
n ward locations | 44 | 38 |
Sequence matches per HOCI case | ||
n sequence matches from same ward, median (IQR, range) | 1 (0–5, 0–12) | 1 (0–4, 0–18) |
n sequence matches from rest of hospital, median (IQR, range) | 3 (1–8, 0–52) | 27 (5–52, 0–150) |
Standard PHE definition of outbreak event | ||
HOCI cases part of ward outbreak event, n (%) | 95 (76.0) | 184 (91.5) |
n ward outbreak events | 17 | 24 |
n HOCI cases per ward outbreak event, median (IQR, range) | 4 (2–8, 2–17) | 5 (3.5–10.5, 2–28) |
Days from first to last case in outbreak, median (IQR, range) | 8 (6–15, 0–31) | 18 (13–34, 3–68) |
n wards with more than one distinct outbreak event | 0 | 0 |
Outbreak events with sequence linkage | ||
HOCI cases part of ward outbreak event, n (%) | 85 (68.0) | 140* (69.7) |
n ward outbreak events | 16 | 33 |
n HOCI cases per ward outbreak event, median (IQR, range) | 3.5 (2–8, 2–16) | 3 (2–4, 1–19) |
Days from first to last case in outbreak, median (IQR, range) | 6 (4–9, 0–15) | 4 (2–8, 0–17) |
n wards with more than one distinct outbreak event | 0 | 9† |
* Includes two HOCIs which each showed a close sequence match to another case on the same ward with interval from admission to sample date ≤2 days.
†In three wards, there were three genetically distinct outbreak events.
HOCI: hospital onset COVID-19 infection; IQR: interquartile range; PHE: Public Health England.
Comma separated value file containing a list of the COG-UK identification codes for viral sequences included in the analysis.
Details of the COVID-19 Genomics UK (COG-UK) consortium.